Detailed information    

insolico Bioinformatically predicted

Overview

Name   pilD   Type   Machinery gene
Locus tag   HKW96_RS25290 Genome accession   NZ_CP053057
Coordinates   5642771..5643643 (+) Length   290 a.a.
NCBI ID   WP_023969387.1    Uniprot ID   -
Organism   Pseudomonas chlororaphis strain RP4     
Function   assembly of type IV pilus (predicted from homology)   
DNA binding and uptake

Genomic Context

Location: 5637771..5648643
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  HKW96_RS25275 (HKW96_25275) - 5640125..5640481 (-) 357 WP_009050906.1 BON domain-containing protein -
  HKW96_RS25280 (HKW96_25280) - 5640769..5641185 (-) 417 WP_009050907.1 pilin -
  HKW96_RS25285 (HKW96_25285) pilC 5641551..5642768 (+) 1218 WP_023969386.1 type II secretion system F family protein Machinery gene
  HKW96_RS25290 (HKW96_25290) pilD 5642771..5643643 (+) 873 WP_023969387.1 A24 family peptidase Machinery gene
  HKW96_RS25295 (HKW96_25295) coaE 5643640..5644263 (+) 624 WP_009045669.1 dephospho-CoA kinase -
  HKW96_RS25300 (HKW96_25300) yacG 5644260..5644463 (+) 204 WP_009045670.1 DNA gyrase inhibitor YacG -
  HKW96_RS25305 (HKW96_25305) - 5644468..5644683 (-) 216 WP_009050911.1 hypothetical protein -
  HKW96_RS25310 (HKW96_25310) - 5644749..5645438 (-) 690 WP_023969388.1 energy-coupling factor ABC transporter permease -
  HKW96_RS25315 (HKW96_25315) - 5645435..5645902 (-) 468 WP_023969389.1 hypothetical protein -
  HKW96_RS25320 (HKW96_25320) - 5646357..5647793 (+) 1437 WP_023969390.1 undecaprenyl-phosphate glucose phosphotransferase -

Sequence

Protein


Download         Length: 290 a.a.        Molecular weight: 32116.30 Da        Isoelectric Point: 7.9954

>NTDB_id=442545 HKW96_RS25290 WP_023969387.1 5642771..5643643(+) (pilD) [Pseudomonas chlororaphis strain RP4]
MSLTEVLASYPLVFVASMLVLGLIVGSFLNVLIWRLPKMLERDWHAQARDILGLPVEPAGPTYNLLLPHSQCPHCAHSIR
PWENIPVFSYLLLRGRCSACQAPIGRRYPLVELTCGLASAFVAWHFGFGWQAFLMLLLSWGLLAMSLIDADHQLLPDVLV
LPLLWLGLIVNGFELFVSLHDALWGAVAGYLCLWSVYWLFKLLTGKEGMGHGDFKLLAMFGAWGGWQILPMTLLLASLTG
ALAGIAMLRRNRAQMSTPIPFGPFLAIAGWIALLWGGQITGSYLQFVGFR

Nucleotide


Download         Length: 873 bp        

>NTDB_id=442545 HKW96_RS25290 WP_023969387.1 5642771..5643643(+) (pilD) [Pseudomonas chlororaphis strain RP4]
ATGTCATTGACTGAGGTCCTGGCCAGCTATCCGCTGGTCTTCGTAGCATCGATGCTGGTCCTGGGCCTGATTGTCGGCAG
CTTTCTCAATGTGCTGATCTGGCGTCTGCCGAAGATGCTCGAGCGCGACTGGCACGCCCAGGCCCGTGACATCCTGGGGC
TGCCCGTCGAGCCTGCCGGGCCGACCTACAACCTGCTGCTCCCGCATTCCCAGTGCCCTCACTGCGCACATTCGATCCGC
CCCTGGGAAAACATCCCGGTGTTCAGCTACCTGCTGCTGCGCGGACGCTGCTCCGCGTGCCAGGCACCGATCGGCCGGCG
CTACCCGCTGGTGGAGCTGACCTGCGGCCTGGCCTCGGCGTTCGTGGCCTGGCATTTCGGCTTTGGCTGGCAGGCCTTCC
TGATGCTGCTGCTGAGCTGGGGCCTGTTGGCAATGAGCCTGATCGATGCCGATCATCAGCTGTTGCCCGACGTGCTGGTG
CTGCCGCTGTTGTGGCTGGGCCTGATCGTCAATGGCTTCGAGCTGTTCGTCAGCCTCCATGATGCGCTGTGGGGCGCCGT
GGCCGGCTACCTGTGCCTGTGGTCGGTGTACTGGTTGTTCAAGCTGCTGACCGGCAAGGAAGGCATGGGGCACGGCGATT
TCAAGCTGCTGGCCATGTTCGGCGCCTGGGGCGGCTGGCAGATTCTGCCGATGACCCTGCTGCTGGCCTCACTGACAGGA
GCCCTGGCCGGGATCGCCATGCTGCGCCGCAACCGTGCGCAAATGTCCACGCCTATCCCTTTCGGTCCCTTTCTGGCCAT
TGCCGGCTGGATTGCCTTGCTCTGGGGTGGTCAAATAACCGGCTCCTATTTGCAGTTTGTCGGTTTCAGATGA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(137-245)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(20-126)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure

Transmembrane helices

Transmembrane helices of protein were predicted by TMHMM 2.0 and visualized by seqviz and ECharts.


Visualization of predicted probability:


Similar proteins

Only experimentally validated proteins are listed.

Protein Organism Identities (%) Coverage (%) Ha-value
  pilD Vibrio cholerae strain A1552

52.465

97.931

0.514
  pilD Vibrio campbellii strain DS40M4

52.297

97.586

0.51
  pilD Acinetobacter baumannii D1279779

50.545

94.828

0.479
  pilD Acinetobacter nosocomialis M2

49.818

94.828

0.472
  pilD Neisseria gonorrhoeae MS11

48.162

93.793

0.452